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At least 109 records · Page 6
All sourcesNASA NTRSDOE OSTI
DOE OSTI2021

Development of energetic and enzymatic limitations on microbial carbon cycling in soils

Soil organic carbon (SOC) constitutes an important reservoir in the global carbon cycle that is vulnerable to transformation and loss from land use and climate change. Anoxic conditions protect SOC from microbial degradation through limiting the energetics of respiration and inhibiting extracellular oxidative enzymes. Given growing evidence of prevalent anaerobic microsites in upland soils, we designed an experiment testing the development of dissolved organic carbon (DOC) signatures of energetic and enzymatic limitations on microbial carbon utilization across simulated soil aggregates or peds. Reactors comprised a soil column “aggregate” underlying an advective “macropore” channel. Soils received downward diffusive inputs of aerated porewater media with added nitrate, sulfate, or no amendment—where native ferrihydrite served as dominant anaerobic terminal electron acceptor (TEA). After 40 days, added nitrate resulted in highest bulk respiration and DOC production while sulfate did not differ from the control. Nominal oxidation state of carbon (NOSC) was higher (more favorable) with added TEAs at soil surfaces and decreased with depth, while NOSC in the non-amended soil remained lower and constant with depth. DOC generally increased with depth, which along with decreasing NOSC values indicates joint electron-donor and acceptor control over respiration energetics. Of all organic compound classes, only the relative abundance of phenolics increased between 0 and 0.5 cm depth, which aligns with the oxic-anoxic transition and suggests oxidative enzyme inhibition. Furthermore, our results suggest that oxygen limitation within upland soil aggregates may preserve SOC via both energetic and enzymatic C protection mechanisms, which are vulnerable upon exposure to oxygen.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

Variation in Root Exudate Composition Influences Soil Microbiome Membership and Function

Root exudation is one of the primary processes that mediate interactions between plant roots, microorganisms, and the soil matrix, yet the mechanisms by which exudation alters microbial metabolism in soils have been challenging to unravel. Here, utilizing distinct sorghum genotypes, we characterized the chemical heterogeneity between root exudates and the effects of that variability on soil microbial membership and metabolism. Distinct exudate chemical profiles were quantified and used to formulate synthetic root exudate treatments: a high-organic-acid treatment (HOT) and a high-sugar treatment (HST). To parse the response of the soil microbiome to different exudate regimens, laboratory soil reactors were amended with these root exudate treatments as well as a nonexudate control. Amplicon sequencing of the 16S rRNA gene illustrated distinct microbial diversity patterns and membership in response to HST, HOT, or control amendments. Exometabolite changes reflected these microbial community changes, and we observed enrichment of organic and amino acids, as well as possible phytohormones in the HST relative to the HOT and control. Linking the metabolic capacity of metagenome-assembled genomes in the HST to the exometabolite patterns, we identified microorganisms that could produce these phytohormones. Our findings emphasize the tractability of high-resolution multiomics tools to investigate soil microbiomes, opening the possibility of manipulating native microbial communities to improve specific soil microbial functions and enhance crop production.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2022

A consensus protocol for the recovery of mercury methylation genes from metagenomes

Abstract Mercury (Hg) methylation genes ( hgcAB ) mediate the formation of the toxic methylmercury and have been identified from diverse environments, including freshwater and marine ecosystems, Arctic permafrost, forest and paddy soils, coal‐ash amended sediments, chlor‐alkali plants discharges and geothermal springs. Here we present the first attempt at a standardized protocol for the detection, identification and quantification of hgc genes from metagenomes. Our Hg‐cycling microorganisms in aquatic and terrestrial ecosystems (Hg‐MATE) database, a catalogue of hgc genes, provides the most accurate information to date on the taxonomic identity and functional/metabolic attributes of microorganisms responsible for Hg methylation in the environment. Furthermore, we introduce “marky‐coco”, a ready‐to‐use bioinformatic pipeline based on de novo single‐metagenome assembly, for easy and accurate characterization of hgc genes from environmental samples. We compared the recovery of hgc genes from environmental metagenomes using the marky‐coco pipeline with an approach based on coassembly of multiple metagenomes. Our data show similar efficiency in both approaches for most environments except those with high diversity (i.e., paddy soils) for which a coassembly approach was preferred. Finally, we discuss the definition of true hgc genes and methods to normalize hgc gene counts from metagenomes.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Soil carbon stocks in temperate grasslands differ strongly across sites but are insensitive to decade-long fertilization

We report enhancing soil carbon (C) storage has the potential to offset human-caused increases in atmospheric CO 2 . Rising CO 2 has occurred concurrently with increasing supply rates of biologically limiting nutrients such as nitrogen (N) and phosphorus (P). However, it is unclear how increased supplies of N and P will alter soil C sequestration, particularly in grasslands, which make up nearly a third of non-agricultural land world-wide. Here, we leverage a globally distributed nutrient addition experiment (the Nutrient Network) to examine how a decade of N and P fertilization (alone and in combination) influenced soil C and N stocks at nine grassland sites spanning the continental United States. We measured changes in bulk soil C and N stocks and in three soil C fractions (light and heavy particulate organic matter, and mineral-associated organic matter fractions). Nutrient amendment had variable effects on soil C and N pools that ranged from strongly positive to strongly negative, while soil C and N pool sizes varied by more than an order of magnitude across sites. Piecewise SEM clarified that small increases in plant C inputs with fertilization did not translate to greater soil C storage. Nevertheless, peak season aboveground plant biomass (but not root biomass or production) was strongly positively related to soil C storage at seven of the nine sites, and across all nine sites, soil C covaried with moisture index and soil mineralogy, regardless of fertilization. Overall, we show that site factors such as moisture index, plant productivity, soil texture, and mineralogy were key predictors of cross-site soil C, while nutrient amendment had weaker and site-specific effects on C sequestration. This suggests that prioritizing the protection of highly productive temperate grasslands is critical for reducing future greenhouse gas losses arising from land use change.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2025

Humate Amendment Injection Viability Testing – Supplementary Batch Mixture and Soil Column Studies

Groundwater in the Lost Lake Aquifer Zone (LLAZ) in the Southern Sector of the M-Area Hazardous Waste management Facility (HWMF) is contaminated with chlorinated ethenes, including trichloroethylene (TCE) and tetrachloroethylene (PCE). Treatment of contaminated groundwater with humic acid is being evaluated as a potential corrective action for these volatile organic compounds (VOCs) in the LLAZ in Southern Sector (SRNS, 2019). Pilot scale injections of Huma-K brand humic acid for groundwater treatment were previously performed in M-Area between 2017 and 2020 (Amidon, 2023). Groundwater was extracted from the Lost Lake Aquifer Zone (LLAZ), then a solution of humate was mixed with recovered groundwater and subsequently re-injected into the same aquifer unit. Operations of the historical humate pilot testing were discontinued in 2020 due to COVID-19 restrictions, low injection rates, and recirculation fluid spillage. No further field scale or laboratory research to investigate humate amended groundwater injection was performed at the SRS until 2024. At the request of Area Completion Projects (ACP), the Savannah River National Laboratory (SRNL) performed supplementary testing to help determine the viability of further injection of humate as a remedial option for VOCs within the LLAZ in the Southern Sector of the M-Area HWMF.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗
DOE OSTI2025

Microfluidic droplets with amended culture media cultivate a greater diversity of soil microorganisms

ABSTRACT Uncultivated but abundant soil microorganisms have untapped potential for producing broad ranges of natural products, as well as for bioremediation. However, cultivating soil microorganisms while maintaining a broad microorganism diversity to enable phenotyping and functional analysis of as diverse individual isolates as possible remains challenging. In this study, we developed and tested the ability of several culture media formulations that contain defined soil metabolites or soil extracts to maintain microorganism diversity during culture. We also assessed their performance in microfluidic droplet cultivation where single-soil microorganism isolates were encapsulated and cultivated in picoliter-volume water-in-oil emulsion droplets to enable clonal growth needed for downstream functional analyses. Our results show that droplet cultivation with media supplemented by soil extract or soil metabolites enables the recovery of soil microorganisms with higher diversity (up to 1.5-fold higher richness) compared to bulk cultivation methods. Importantly, 1.7-fold more of less abundant (<1%) phyla and 11-fold more of unique genera were recovered, demonstrating the utility of this method for interrogating highly diverse soil microorganisms for broad ranges of applications. IMPORTANCE Although soil microorganisms hold a significant value in bioproduction and bioremediation, only a small fraction—less than 1%—can be cultured under specific media and cultivation conditions. This indicates that there are ample opportunities in harvesting the diverse environmental microorganisms if isolating and recovering these uncultured microorganisms are possible. This paper presents a new cultivation technique composed of isolating single-soil microorganism cell from anin situsoil microorganism community in microfluidic droplets and conducting in-droplet cultivation in media supplemented by soil extract or soil metabolites. This method enables the recovery of a broader diversity of the original microorganism community, laying the groundwork for a high-throughput phenotyping of these diverse microorganisms from their natural habitats.

Biotechnology & Applied Microbiology↗
DOE OSTI2021

Biochar alters hydraulic conductivity and impacts nutrient leaching in two agricultural soils

Biochar is purported to provide agricultural benefits when added to the soil, through changes in saturated hydraulic conductivity (K sat ) and increased nutrient retention through chemical or physical means. Despite increased interest and investigation, there remains uncertainty regarding the ability of biochar to deliver these agronomic benefits due to differences in biochar feedstock, production method, production temperature, and soil texture. In this project, a suite of experiments was carried out using biochars of diverse feedstocks and production temperatures, in order to determine the biochar parameters which may optimize agricultural benefits. Sorption experiments were performed with seven distinct biochars to determine sorption efficiencies for ammonium and nitrate. Only one biochar effectively retained nitrate, while all biochars bound ammonium. The three biochars with the highest binding capacities (produced from almond shell at 500 and 800 °C (AS500 and AS800) and softwood at 500 °C (SW500)) were chosen for column experiments. Biochars were amended to a sandy loam and a silt loam at 0 % and 2 % (w/w), and K sat was measured. Biochars reduced K sat in both soils by 64 %–80 %, with the exception of AS800, which increased K sat by 98 % in the silt loam. Breakthrough curves for nitrate and ammonium, as well as leachate nutrient concentration, were also measured in the sandy loam columns. All biochars significantly decreased the quantity of ammonium in the leachate, by 22 % to 78 %, and slowed its movement through the soil profile. Ammonium retention was linked to high cation exchange capacity and a high oxygen-to-carbon ratio, indicating that the primary control of ammonium retention in biochar-amended soils is the chemical affinity between biochar surfaces and ammonium. Biochars had little to no effect on the timing of nitrate release, and only SW500 decreased total quantity, by 27 % to 36 %. The ability of biochar to retain nitrate may be linked to high micropore specific surface area, suggesting a physical entrapment rather than a chemical binding. Together, this work sheds new light on the combined chemical and physical means by which biochar may alter soils to impact nutrient leaching and hydraulic conductivity for agricultural production.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Greenhouse gas and dissolved oxygen production and consumption rates associated with Regier et al. (2023)

Tidal inundation along the coastal terrestrial-aquatic interface controls soil and sediment biogeochemistry and gas dynamics. Although a rich literature exist on studies of the influence of tidal waters on the biogeochemistry of coastal ecosystem soils, few studies have experimentally addressed the reverse question: How do soils (or sediments) from different coastal ecosystems influence the biogeochemistry of the tidal waters that inundate them? We conducted short-term microcosm laboratory experiments where seawater was amended with sediments and soils collected across regional gradients of inundation exposure (i.e., frequently to rarely inundated) and measured changes in dissolved oxygen and greenhouse gas concentrations to calculate gas consumption or production rates occurring during seawater exposure to terrestrial materials. This data package contains dissolved oxygen and greenhouse gas data collected during incubation of soils and sediments collected at 18 sites, which were used in the publication Regier et al. (2023) entitled “Coastal inundation regime moderates the short-term effects of sediment and soil additions on seawater oxygen and greenhouse gas dynamics: a microcosm experiment” which is published in Frontiers in Marine Science (DOI: https://doi.org/10.3389/fmars.2023.1308590).---Acknowledging EXCHANGE: General Support and Data Product UseWe ask that users of EXCHANGE data add the following acknowledgement when publishing data in scholarly articles and data repositories:"This research is based on work supported by COMPASS-FME, a multi-institutional project supported by the U.S. Department of Energy, Office of Science, Biological and Environmental Research as part of the Environmental System Science Program."

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Compost Amendment to a Grazed California Annual Grassland Increases Gross Primary Productivity Due To a Longer Growing Season

Abstract Compost amendment to rangelands is a proposed nature‐based climate solution to increase plant productivity and soil carbon sequestration. However, it has not been evaluated using quasicontinuous ecosystem‐scale measurements. Here, we present the first study to utilize eddy covariance and footprint partitioning to monitor carbon exchange in a grassland with and without compost amendment, monitoring for 1 year before and 1 year after treatment. Compost amendment to an annual California grassland was found to enhance net ecosystem removal of carbon. Our study confirmed that compost‐amended grasslands, similar to nonamended grasslands, are net carbon sources to the atmosphere; however, the amendment appears to be slowing down the rate at which these ecosystems lose carbon by 0.71 Mg C ha −1 per growing season. Digital repeated imagery of the canopy revealed that compost‐amended grasslands experienced an earlier green‐up, resulting in an overall longer growing season by >60 days. Notably, we did not detect significantly higher amounts of soil carbon in compost‐amended soils. High variability in soil carbon demands greater sampling replication in future studies. A longer growing season and higher productivity are hypothesized to be a result of greater availability of macronutrients and micronutrients in the top layer of soil (specifically nitrogen, phosphorus, and zinc).

Fenster, Tommy L. D.↗
DOE OSTI2023

Coastal inundation regime moderates the short-term effects of sediment and soil additions on seawater oxygen and greenhouse gas dynamics: a microcosm experiment

The frequency and persistence of tidal inundation varies along the coastal terrestrial-aquatic interface, from frequently inundated wetlands to rarely inundated upland forests. This inundation gradient controls soil and sediment biogeochemistry and influence the exchange of soils and sediments from terrestrial to aquatic domains. Although a rich literature exist on studies of the influence of tidal waters on the biogeochemistry of coastal ecosystem soils, few studies have experimentally addressed the reverse question: How do soils (or sediments) from different coastal ecosystems influence the biogeochemistry of the tidal waters that inundate them? To better understand initial responses of coastal waters that flood coastal wetlands and uplands, we conducted short-term laboratory experiments where seawater was amended with sediments and soils collected across regional gradients of inundation exposure (i.e., frequently to rarely inundated) for 14 sites across the Mid-Atlantic, USA. Measured changes in dissolved oxygen and greenhouse gas concentrations were used to calculate gas consumption or production rates occurring during seawater exposure to terrestrial materials. We also measured soil and water physical and chemical properties to explore potential drivers. We observed higher oxygen consumption rates for seawater incubated with soils/sediments from frequently inundated locations and higher carbon dioxide production for seawater incubated with soils from rarely inundated transect locations. Incubations with soil from rarely inundated sites produced the highest global warming potential, primarily driven by carbon dioxide and secondarily by nitrous oxide. We also found environmental drivers of gas rates varied notably between transect locations. Our findings indicate that seawater responses to soil and sediment inputs across coastal terrestrial-aquatic interfaces exhibit some consistent patterns and high intra- and inter-site variability, suggesting potential biogeochemical feedback loops as inundation regimes shift inland.

coastal inundation↗
DOE OSTI2021

Microbial Community Shifts Reflect Losses of Native Soil Carbon with Pyrogenic and Fresh Organic Matter Additions and Are Greatest in Low-Carbon Soils

ABSTRACT Soil organic carbon (SOC) plays an important role in regulating global climate change, carbon and nutrient cycling in soils, and soil moisture. Organic matter (OM) additions to soils can affect the rate at which SOC is mineralized by microbes, with potentially important effects on SOC stocks. Understanding how pyrogenic organic matter (PyOM) affects the cycling of native SOC (nSOC) and the soil microbes responsible for these effects is important for fire-affected ecosystems as well as for biochar-amended systems. We used an incubation trial with five different soils from National Ecological Observatory Network sites across the United States and 13 C-labeled 350°C corn stover PyOM and fresh corn stover OM to trace nSOC-derived CO 2 emissions with and without PyOM and OM amendments. We used high-throughput sequencing of rRNA genes to characterize bacterial, archaeal, and fungal communities and their responses to PyOM and OM in soils that were previously stored at −80°C. We found that the effects of amendments on nSOC-derived CO 2 reflected the unamended soil C status, where relative increases in C mineralization were greatest in low-C soils. OM additions produced much greater effects on nSOC-CO 2 emissions than PyOM additions. Furthermore, the magnitude of the microbial community composition change mirrored the magnitude of increases in nSOC-CO 2 , indicating that a specific subset of microbes was likely responsible for the observed changes in nSOC mineralization. However, PyOM responders differed across soils and did not necessarily reflect a common “charosphere.” Overall, this study suggests that soils that already have low SOC may be particularly vulnerable to short-term increases in SOC loss with OM or PyOM additions. IMPORTANCE Soil organic matter (SOM) has an important role in global climate change, carbon and nutrient cycling in soils, and soil moisture dynamics. Understanding the processes that affect SOM stocks is important for managing these functions. Recently, understanding how fire-affected organic matter (or “pyrogenic” organic matter [PyOM]) affects existing SOM stocks has become increasingly important, due to both changing fire regimes and interest in “biochar,” pyrogenic organic matter that is produced intentionally for carbon management or as an agricultural soil amendment. We found that soils with less SOM were more prone to increased losses with PyOM (and fresh organic matter) additions and that soil microbial communities changed more in soils that also had greater SOM losses with PyOM additions. This suggests that soils that already have low SOM content may be particularly vulnerable to short-term increases in SOM loss and that a subset of the soil microbial community is likely responsible for these effects.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2024

Microbial Proxies for Anoxic Microsites Vary with Management and Partially Explain Soil Carbon Concentration

Anoxic microsites are potentially important but unresolved contributors to soil organic carbon (C) storage. How anoxic microsites vary with soil management and the degree to which anoxic microsites contribute to soil C stabilization remain unknown. Sampling from four long-term agricultural experiments in the central United States, we examined how anoxic microsites varied with management (e.g., cultivation, tillage, and manure amendments) and whether anoxic microsites determine soil C concentration in surface (0–15 cm) soils. We used a novel approach to track anaerobe habitat space and, hence, anoxic microsites using DNA copies of anaerobic functional genes over a confined volume of soil. No-till practices inconsistently increased anoxic microsite extent compared to conventionally tilled soils, and within one site organic matter amendments increased anaerobe abundance in no-till soils. Across all long-term tillage trials, uncultivated soils had ~2–4 times more copies of anaerobic functional genes than their cropland counterparts. Finally, anaerobe abundance was positively correlated to soil C concentration. Even when accounting for other soil C protection mechanisms, anaerobe abundance, our proxy for anoxic microsites, explained 41% of the variance and 5% of the unique variance in soil C concentration in cropland soils, making anoxic microsites the strongest management-responsive predictor of soil C concentration. Our results suggest that careful management of anoxic microsites may be a promising strategy to increase soil C storage within agricultural soils.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2022

The climate change mitigation potential of annual grasslands under future climates

Abstract Composted manure and green waste amendments have been shown to increase net carbon (C) sequestration in rangeland soils and have been proposed as a means to help lower atmospheric CO 2 concentrations. However, the effect of climate change on soil organic C (SOC) stocks and greenhouse gas emissions in rangelands is not well understood, and the viability of climate change mitigation strategies under future conditions is even less certain. We used a process‐based biogeochemical model (DayCent) at a daily time step to explore the long‐term effects of potential future climate changes on C and greenhouse gas dynamics in annual grassland ecosystems. We then used the model to explore how the same ecosystems might respond to climate change following compost amendments to soils and determined the long‐term viability of net SOC sequestration under changing climates. We simulated net primary productivity (NPP), SOC, and greenhouse gas fluxes across seven California annual grasslands with and without compost amendments. We drove the DayCent simulations with field data and with site‐specific daily climate data from two Earth system models (CanESM2 and HadGEM‐ES) and two representative concentration pathways (RCP4.5 and RCP8.5) through 2100. NPP and SOC stocks in unamended and amended ecosystems were surprisingly insensitive to projected climate changes. A one‐time amendment of compost to rangeland acted as a slow‐release organic fertilizer and increased NPP by up to 390–814 kg C ha −1 year −1 across sites. The amendment effect on NPP was not sensitive to Earth system model or emissions scenario and endured through the end of the century. Net SOC sequestration amounted to 1.96 ± 0.02 Mg C ha −1 relative to unamended soils at the maximum amendment effect. Averaged across sites and scenarios, SOC sequestration peaked 22 ± 1 years after amendment and declined but remained positive throughout the century. Though compost stimulated nitrous oxide (N 2 O) emissions, the cumulative net emissions (in CO 2 equivalents) due to compost were far less than the amount of SOC sequestered. Compost amendments resulted in a net climate benefit of 69.6 ± 0.5 Tg CO 2 e 20 ± 1 years after amendment if applied to similar ecosystems across the state, amounting to 39% of California's rangeland. These results suggest that the biogeochemical benefits of a single amendment of compost to rangelands in California are insensitive to climate change and could contribute to decadal‐scale climate change mitigation goals alongside emissions reductions.

Mayer, Allegra↗
DOE OSTI2020

Lignin lags, leads, or limits the decomposition of litter and soil organic carbon

Lignin’s role in litter and soil organic carbon (SOC) decomposition remains contentious. Lignin decomposition was traditionally thought to increase during midstage litter decomposition, when cellulose occlusion by lignin began to limit mass loss. Alternatively, lignin decomposition could be greatest in fresh litter as a consequence of co-metabolism, and lignin might decompose faster than bulk SOC. To test these competing hypotheses, we incubated 10 forest soils with C 4 grass litter (amended with 13 C-labeled or unlabeled lignin) over 2 yr and measured soil respiration and its isotope composition. Early lignin decomposition was greatest in 5 of 10 soils, consistent with the co-metabolism hypothesis. However, lignin decomposition peaked 6–24 months later in the other five soils, consistent with the substrate-limitation hypothesis; these soils were highly acidic. Rates of lignin, litter, and SOC decomposition tended to converge over time. Cumulative lignin decomposition was never greater than SOC decomposition; lignin decomposition was significantly lower than SOC decomposition in six soils. Net nitrogen mineralization predicted lignin decomposition ratios relative to litter and SOC. Although the onset of lignin decomposition can indeed be rapid, lignin still presents a likely bottleneck in litter and SOC decomposition, meriting a reconsideration of lignin’s role in modern decomposition paradigms.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Trace Metal Content and Speciation, Water and Soil Chemistry, and Methane Production for a Wetland in Missouri (September 2015) and in Florida (January 2016)

Data is associated with a manuscript in preparation for submission to explore whether low trace metal availability inhibits methane production in freshwater wetland soils. Reported data are from two field sites, one in Missouri and the second in Florida (see location data). At each site, surface water compositions and properties and soil compositions are reported. Trace metal availability is assessed via sequential chemical extractions, Ni K-edge X-ray absorption near edge structure (XANES) spectroscopy, and X-ray microfluorescence imaging. Soil mineralogy is determined via powder X-ray diffraction. Multi-energy X-ray microfluorescence imaging as well as bulk and microscale S K-edge XANES spectra assess sulfur speciation in the soils. This package also reports data from trace metal amendment experiments, specifically methane (CH4) production versus time in soil incubations, the dissolved trace metal concentrations in these incubations, and the Ni K-edge XANES and extended X-ray absorption fine structure (EXAFS) spectra of soils to which increasing concentrations of Ni were added. A final version of this package will be published upon acceptance of the associated manuscript.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2020

Deconstructing the Soil Microbiome into Reduced-Complexity Functional Modules

The soil microbiome is an invaluable component of the biosphere and critical for ecosystem functions, including biogeochemical cycling, soil-atmosphere gas exchange, degradation of toxic compounds, and promotion of plant growth and stress resistance/resilience. An improved understanding of the soil microbiome will help with predicting how these processes respond to external perturbations, and with harnessing beneficial aspects of the soil microbiome for agronomic applications such as crop amendments. However, the extensive taxonomic and functional diversity inherent within the soil microbiome hinders efficient analysis of this system. Microbial biodiversity in soils is orders of magnitude greater than other commonly studied systems such as the human gut microbiome (Blum, Zechmeister-Boltenstern, and Keiblinger 2019; Berendsen, Pieterse, and Bakker 2012). Thousands of microbial taxa may be found in a single gram of soil (Roesch et al. 2007), and high rates of gene flow and mutation further promote microbial diversification (Sergaki et al. 2018). Concomitantly, functional diversity in soil is similarly extensive. Soil is a heterogeneous mixture of microenvironments with defined physical and chemical attributes (Bach et al. 2018), within which numerous microbial guilds of distinct life-strategies and metabolic capacities can be found (Perez-Garcia, Lear, and Singhal 2016; H.-S. Song et al. 2014). Furthermore, the soil microbiome harbors a significant fraction of rare and/or quiescent members (Blagodatskaya and Kuzyakov 2013) that exist below the threshold of detection of current technologies. Such rare taxa may make significant contributions to process rates (Shade and Gilbert 2015; Dawson et al. 2017), but their scarcity complicates their identification and analysis. Finally, the vast amounts of information generated through holistic analyses of soil communities represent an intense computational burden (Scholz, Lo, and Chain 2012; Prosser 2015) that precludes assessment of the complete functional and taxonomic diversity contained in this ecosystem.

Naylor, Dan T.↗
DOE OSTI2023

Lawrence Livermore National Laboratory Experimental Test Site 300: Energetic Materials Development Enclave (EMDEC) Soil Sampling and Analysis Plan Addendum 1 (April 2023)

The purpose of this addendum is to amend and update the Energetic Materials Development Enclave [project] Soil Sampling and Analysis Plan (SAP) dated June 2022 (LLNL-AM-22- 21678). In July 2022, portions of the SAP were completed. Since then, the project scope and limits have been redefined to include potential additional buildings. The exact locations of the additional buildings have not been determined, but the Project Management Office (PMO) would like to investigate at this time additional areas adjacent to the investigation area subject to the June 2022 SAP. The information contained in this addendum supersedes the June 2022 SAP. However, this addendum only addresses elements of the June 2022 SAP that were modified. Elements of the June 2022 SAP that have not been modified are relevant and will remain in effect.

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2021

Nutrients cause consolidation of soil carbon flux to small proportion of bacterial community

Nutrient amendment diminished bacterial functional diversity, consolidating carbon flow through fewer bacterial taxa. Here, we show strong differences in the bacterial taxa responsible for respiration from four ecosystems, indicating the potential for taxon-specific control over soil carbon cycling. Trends in functional diversity, defined as the richness of bacteria contributing to carbon flux and their equitability of carbon use, paralleled trends in taxonomic diversity although functional diversity was lower overall. Among genera common to all ecosystems, Bradyrhizobium, the Acidobacteria genus RB41, and Streptomyces together composed 45–57% of carbon flow through bacterial productivity and respiration. Bacteria that utilized the most carbon amendment (glucose) were also those that utilized the most native soil carbon, suggesting that the behavior of key soil taxa may influence carbon balance. Mapping carbon flow through different microbial taxa as demonstrated here is crucial in developing taxon-sensitive soil carbon models that may reduce the uncertainty in climate change projections.

59 BASIC BIOLOGICAL SCIENCES↗